BioSimSpace.Process.Amber¶

class BioSimSpace.Process.Amber(system, protocol, reference_system=None, explicit_dummies=False, exe=None, is_gpu=False, name='amber', work_dir=None, seed=None, extra_options={}, extra_lines=[], extra_args={}, property_map={}, **kwargs)[source]¶

A class for running simulations using AMBER.

__init__(system, protocol, reference_system=None, explicit_dummies=False, exe=None, is_gpu=False, name='amber', work_dir=None, seed=None, extra_options={}, extra_lines=[], extra_args={}, property_map={}, **kwargs)[source]¶

Constructor.

Parameters:

system (System) – The molecular system.
protocol (Protocol) – The protocol for the AMBER process.
reference_system (System or None) – An optional system to use as a source of reference coordinates for position restraints. It is assumed that this system has the same topology as “system”. If this is None, then “system” is used as a reference.
explicit_dummies (bool) – Whether to keep dummy atoms explicit at alchemical end states, or remove them.
exe (str) – The full path to the AMBER executable.
is_gpu (bool) – Whether to use the GPU accelerated version of AMBER.
name (str) – The name of the process.
work_dir – The working directory for the process.
seed (int) – A random number seed.
extra_options (dict) – A dictionary containing extra options. Overrides the defaults generated by the protocol.
extra_lines ([str]) – A list of extra lines to put at the end of the configuration file.
extra_args (dict) – A dictionary of extra command-line arguments to pass to the AMBER executable.
property_map (dict) – A dictionary that maps system “properties” to their user defined values. This allows the user to refer to properties with their own naming scheme, e.g. { “charge” : “my-charge” }
kwargs (dict) – Additional keyword arguments.

Methods

`__init__`(system, protocol[, ...])	Constructor.
`addArgs`(args)	Append additional command-line arguments.
`addToConfig`(config)	Add a string to the configuration list.
`clearArgs`()	Clear all of the command-line arguments.
`command`()	Return the command-line string used to run the process.
`deleteArg`(arg)	Delete an argument from the dictionary.
`exe`()	Return the executable.
`getAngleEnergy`([time_series, region, ...])	Get the angle energy.
`getArgString`()	Get the command-line arguments string.
`getArgStringList`()	Convert the argument dictionary into a list of strings.
`getArgs`()	Get the dictionary of command-line arguments.
`getBondEnergy`([time_series, region, ...])	Get the bond energy.
`getCentreOfMassKineticEnergy`([time_series, ...])	Get the kinetic energy of the centre of mass in translation.
`getConfig`()	Get the list of configuration file strings.
`getCurrentAngleEnergy`([time_series, region, ...])	Get the current angle energy.
`getCurrentBondEnergy`([time_series, region, ...])	Get the current bond energy.
`getCurrentCentreOfMassKineticEnergy`([...])	Get the current kinetic energy of the centre of mass in translation.
`getCurrentDVDL`([time_series, region, soft_core])	Get the current gradient of the total energy with respect to lambda.
`getCurrentDensity`([time_series, region, ...])	Get the current density.
`getCurrentDihedralEnergy`([time_series, ...])	Get the current total dihedral energy (proper + improper).
`getCurrentElectrostaticEnergy`([time_series, ...])	Get the current dihedral energy.
`getCurrentElectrostaticEnergy14`([...])	Get the current electrostatic energy between atoms 1 and 4.
`getCurrentHydrogenBondEnergy`([time_series, ...])	Get the current hydrogen bond energy.
`getCurrentKineticEnergy`([time_series, ...])	Get the current kinetic energy.
`getCurrentNonBondedEnergy14`([time_series, ...])	Get the current non-bonded energy between atoms 1 and 4.
`getCurrentPotentialEnergy`([time_series, ...])	Get the current potential energy.
`getCurrentPressure`([time_series, region, ...])	Get the current pressure.
`getCurrentRecord`(key[, time_series, unit, ...])	Get a current record from the stdout dictionary.
`getCurrentRecords`([region, soft_core])	Return the current dictionary of stdout time-series records.
`getCurrentRestraintEnergy`([time_series, ...])	Get the current restraint energy.
`getCurrentStep`([time_series, region, soft_core])	Get the current number of integration steps.
`getCurrentSystem`()	Get the latest molecular system.
`getCurrentTemperature`([time_series, region, ...])	Get the current temperature.
`getCurrentTime`([time_series, region, soft_core])	Get the current simulation time.
`getCurrentTotalEnergy`([time_series, region, ...])	Get the current total energy.
`getCurrentVanDerWaalsEnergy`([time_series, ...])	Get the current Van der Vaals energy.
`getCurrentVanDerWaalsEnergy14`([time_series, ...])	Get the current Van der Vaals energy between atoms 1 and 4.
`getCurrentVirial`([time_series, region, ...])	Get the current virial.
`getCurrentVolume`([time_series, region, ...])	Get the current volume.
`getDVDL`([time_series, region, soft_core, block])	Get the gradient of the total energy with respect to lambda.
`getDensity`([time_series, region, soft_core, ...])	Get the density.
`getDihedralEnergy`([time_series, region, ...])	Get the total dihedral energy (proper + improper).
`getElectrostaticEnergy`([time_series, ...])	Get the electrostatic energy.
`getElectrostaticEnergy14`([time_series, ...])	Get the electrostatic energy between atoms 1 and 4.
`getFrame`(index)	Return a specific trajectory frame.
`getHydrogenBondEnergy`([time_series, region, ...])	Get the hydrogen bond energy.
`getInput`([name, file_link])	Return a link to a zip file containing the input files used by the process.
`getKineticEnergy`([time_series, region, ...])	Get the kinetic energy.
`getName`()	Return the process name.
`getNonBondedEnergy14`([time_series, region, ...])	Get the non-bonded energy between atoms 1 and 4.
`getOutput`([name, block, file_link])	Return a link to a zip file of the working directory.
`getPackageName`()	Return the package name.
`getPotentialEnergy`([time_series, region, ...])	Get the potential energy.
`getPressure`([time_series, region, ...])	Get the pressure.
`getRecord`(key[, time_series, unit, region, ...])	Get a record from the stdout dictionary.
`getRecordKey`(record[, region, soft_core])
`getRecords`([region, soft_core, block])	Return the dictionary of stdout time-series records.
`getRestraintEnergy`([time_series, region, ...])	Get the restraint energy.
`getSeed`()	Return the random number seed.
`getStderr`([block])	Return the entire stderr for the process as a list of strings.
`getStdout`([block])	Return the entire stdout for the process as a list of strings.
`getStep`([time_series, region, soft_core, block])	Get the number of integration steps.
`getSystem`([block])	Get the latest molecular system.
`getTemperature`([time_series, region, ...])	Get the temperature.
`getTime`([time_series, region, soft_core, block])	Get the simulation time.
`getTotalEnergy`([time_series, region, ...])	Get the total energy.
`getTrajectory`([backend, block])	Return a trajectory object.
`getVanDerWaalsEnergy`([time_series, region, ...])	Get the Van der Vaals energy.
`getVanDerWaalsEnergy14`([time_series, ...])	Get the Van der Vaals energy between atoms 1 and 4.
`getVirial`([time_series, region, soft_core, ...])	Get the virial.
`getVolume`([time_series, region, soft_core, ...])	Get the volume.
`inputFiles`()	Return the list of input files.
`insertArg`(arg, value, index)	Insert a command-line argument at a specific index.
`isError`()	Return whether the process exited with an error.
`isQueued`()	Return whether the process is queued.
`isRunning`()	Return whether the process is running.
`kill`()	Kill the running process.
`resetArgs`()	Reset the command-line arguments.
`resetConfig`()	Reset the configuration parameters.
`run`([system, protocol, auto_start, restart])	Create and run a new process.
`runTime`()	Return the running time for the process (in minutes).
`setArg`(arg, value)	Set a specific command-line argument.
`setArgs`(args)	Set the dictionary of command-line arguments.
`setConfig`(config)	Set the list of configuration file strings.
`setName`(name)	Set the process name.
`setSeed`(seed)	Set the random number seed.
`start`()	Start the AMBER process.
`stderr`([n])	Print the last n lines of the stderr buffer.
`stdout`([n])	Print the last n lines of the stdout buffer.
`wait`([max_time])	Wait for the process to finish.
`workDir`()	Return the working directory.
`writeConfig`(file)	Write the configuration to file.

addArgs(args)¶

Append additional command-line arguments.

Parameters:: args (dict, collections.OrderedDict) – A dictionary of command line arguments.

addToConfig(config)¶

Add a string to the configuration list.

Parameters:: config (str, [ str ]) – A configuration string, a list of configuration strings, or a path to a configuration file.

clearArgs()¶: Clear all of the command-line arguments.

command()¶

Return the command-line string used to run the process.

Returns:: command – The command string.
Return type:: str

deleteArg(arg)¶

Delete an argument from the dictionary.

Parameters:: arg (str) – The argument to delete.

exe()¶

Return the executable.

Returns:: exe – The path to the executable.
Return type:: str

getAngleEnergy(time_series=False, region=0, soft_core=False, block='AUTO')[source]¶

Get the angle energy.

Parameters:

time_series (bool) – Whether to return a list of time series records.
region (int) – The region to which the record corresponds. There will only be more than one region for FreeEnergy protocols, where 1 indicates the second TI region.
soft_core (bool) – Whether to get the record for the soft-core part of the system for the chosen region.
block (bool) – Whether to block until the process has finished running.

Returns:

energy – The angle energy.

Return type:

Energy

getArgString()¶

Get the command-line arguments string.

Returns:: arg_string – The command-line argument string.
Return type:: str

getArgStringList()¶

Convert the argument dictionary into a list of strings.

Returns:: arg_string_list – The list of command-line arguments.
Return type:: [str]

getArgs()¶

Get the dictionary of command-line arguments.

Returns:: args – The dictionary of command-line arguments.
Return type:: collections.OrderedDict

getBondEnergy(time_series=False, region=0, soft_core=False, block='AUTO')[source]¶

Get the bond energy.

Parameters:

time_series (bool) – Whether to return a list of time series records.
soft_core (bool) – Whether to get the record for the soft-core part of the system for the chosen region.
block (bool) – Whether to block until the process has finished running.

Returns:

energy – The bond energy.

Return type:

Energy

getCentreOfMassKineticEnergy(time_series=False, region=0, soft_core=False, block='AUTO')[source]¶

Get the kinetic energy of the centre of mass in translation.

Parameters:

time_series (bool) – Whether to return a list of time series records.
region (int) – The region to which the record corresponds. There will only be more than one region for FreeEnergy protocols, where 1 indicates the second TI region.
soft_core (bool) – Whether to get the record for the soft-core part of the system for the chosen region.
block (bool) – Whether to block until the process has finished running.

Returns:

energy – The centre of mass kinetic energy.

Return type:

Energy

getConfig()¶

Get the list of configuration file strings.

Returns:: config – The list of configuration strings.
Return type:: [str]

getCurrentAngleEnergy(time_series=False, region=0, soft_core=False)[source]¶

Get the current angle energy.

Parameters:

time_series (bool) – Whether to return a list of time series records.
region (int) – The region to which the record corresponds. There will only be more than one region for FreeEnergy protocols, where 1 indicates the second TI region.
soft_core (bool) – Whether to get the record for the soft-core part of the system for the chosen region.

Returns:

energy – The angle energy.

Return type:

Energy

getCurrentBondEnergy(time_series=False, region=0, soft_core=False)[source]¶

Get the current bond energy.

Parameters:

time_series (bool) – Whether to return a list of time series records.
region (int) – The region to which the record corresponds. There will only be more than one region for FreeEnergy protocols, where 1 indicates the second TI region.
soft_core (bool) – Whether to get the record for the soft-core part of the system for the chosen region.

Returns:

energy – The bond energy.

Return type:

Energy

getCurrentCentreOfMassKineticEnergy(time_series=False, region=0, soft_core=False)[source]¶

Get the current kinetic energy of the centre of mass in translation.

Parameters:

time_series (bool) – Whether to return a list of time series records.
region (int) – The region to which the record corresponds. There will only be more than one region for FreeEnergy protocols, where 1 indicates the second TI region.
soft_core (bool) – Whether to get the record for the soft-core part of the system for the chosen region.

Returns:

energy – The centre of mass kinetic energy.

Return type:

Energy

getCurrentDVDL(time_series=False, region=0, soft_core=False)[source]¶

Get the current gradient of the total energy with respect to lambda.

Parameters:

time_series (bool) – Whether to return a list of time series records.
region (int) – The region to which the record corresponds. There will only be more than one region for FreeEnergy protocols, where 1 indicates the second TI region.
soft_core (bool) – Whether to get the record for the soft-core part of the system for the chosen region.

Returns:

dv_dl – The current gradient of the total energy with respect to lambda.

Return type:

float

getCurrentDensity(time_series=False, region=0, soft_core=False)[source]¶

Get the current density.

Parameters:

time_series (bool) – Whether to return a list of time series records.
region (int) – The region to which the record corresponds. There will only be more than one region for FreeEnergy protocols, where 1 indicates the second TI region.
soft_core (bool) – Whether to get the record for the soft-core part of the system for the chosen region.

Returns:

density – The density.

Return type:

float

getCurrentDihedralEnergy(time_series=False, region=0, soft_core=False)[source]¶

Get the current total dihedral energy (proper + improper).

Parameters:

time_series (bool) – Whether to return a list of time series records.
region (int) – The region to which the record corresponds. There will only be more than one region for FreeEnergy protocols, where 1 indicates the second TI region.
soft_core (bool) – Whether to get the record for the soft-core part of the system for the chosen region.

Returns:

energy – The total dihedral energy.

Return type:

Energy

getCurrentElectrostaticEnergy(time_series=False, region=0, soft_core=False)[source]¶

Get the current dihedral energy.

Parameters:

time_series (bool) – Whether to return a list of time series records.
region (int) – The region to which the record corresponds. There will only be more than one region for FreeEnergy protocols, where 1 indicates the second TI region.
soft_core (bool) – Whether to get the record for the soft-core part of the system for the chosen region.

Returns:

energy – The electrostatic energy.

Return type:

Energy

getCurrentElectrostaticEnergy14(time_series=False, region=0, soft_core=False)[source]¶

Get the current electrostatic energy between atoms 1 and 4.

Parameters:

time_series (bool) – Whether to return a list of time series records.
region (int) – The region to which the record corresponds. There will only be more than one region for FreeEnergy protocols, where 1 indicates the second TI region.
soft_core (bool) – Whether to get the record for the soft-core part of the system for the chosen region.

Returns:

energy – The electrostatic energy between atoms 1 and 4.

Return type:

Energy

getCurrentHydrogenBondEnergy(time_series=False, region=0, soft_core=False)[source]¶

Get the current hydrogen bond energy.

Parameters:

time_series (bool) – Whether to return a list of time series records.
region (int) – The region to which the record corresponds. There will only be more than one region for FreeEnergy protocols, where 1 indicates the second TI region.
soft_core (bool) – Whether to get the record for the soft-core part of the system for the chosen region.

Returns:

energy – The hydrogen bond energy.

Return type:

Energy

getCurrentKineticEnergy(time_series=False, region=0, soft_core=False)[source]¶

Get the current kinetic energy.

Parameters:

time_series (bool) – Whether to return a list of time series records.
region (int) – The region to which the record corresponds. There will only be more than one region for FreeEnergy protocols, where 1 indicates the second TI region.
soft_core (bool) – Whether to get the record for the soft-core part of the system for the chosen region.

Returns:

energy – The kinetic energy.

Return type:

Energy

getCurrentNonBondedEnergy14(time_series=False, region=0, soft_core=False)[source]¶

Get the current non-bonded energy between atoms 1 and 4.

Parameters:

time_series (bool) – Whether to return a list of time series records.
region (int) – The region to which the record corresponds. There will only be more than one region for FreeEnergy protocols, where 1 indicates the second TI region.
soft_core (bool) – Whether to get the record for the soft-core part of the system for the chosen region.

Returns:

energy – The non-bonded energy between atoms 1 and 4.

Return type:

Energy

getCurrentPotentialEnergy(time_series=False, region=0, soft_core=False)[source]¶

Get the current potential energy.

Parameters:

time_series (bool) – Whether to return a list of time series records.
region (int) – The region to which the record corresponds. There will only be more than one region for FreeEnergy protocols, where 1 indicates the second TI region.
soft_core (bool) – Whether to get the record for the soft-core part of the system for the chosen region.

Returns:

energy – The potential energy.

Return type:

Energy

getCurrentPressure(time_series=False, region=0, soft_core=False)[source]¶

Get the current pressure.

Parameters:

time_series (bool) – Whether to return a list of time series records.
region (int) – The region to which the record corresponds. There will only be more than one region for FreeEnergy protocols, where 1 indicates the second TI region.
soft_core (bool) – Whether to get the record for the soft-core part of the system for the chosen region.

Returns:

pressure – The pressure.

Return type:

Pressure

getCurrentRecord(key, time_series=False, unit=None, region=0, soft_core=False)[source]¶

Get a current record from the stdout dictionary.

Parameters:

key (str) – A universal record key based on the key used in the AMBER standard output. Use ‘getRecordKey(record)` to generate the key. The records are those used in the AMBER standard output, e.g. ‘TEMP(K)’. Please consult the current AMBER manual for details: https://ambermd.org/Manuals.php
time_series (bool) – Whether to return a list of time series records.
unit (Unit) – The unit to convert the record to.
region (int) – The region to which the record corresponds. There will only be more than one region for FreeEnergy protocols, where 1 indicates the second TI region.
soft_core (bool) – Whether to get the record for the soft-core part of the system for the chosen region.

Returns:

record – The matching record.

Return type:

Type

getCurrentRecords(region=0, soft_core=False)[source]¶

Return the current dictionary of stdout time-series records.

Parameters:

region (int) – The region to which the record corresponds. There will only be more than one region for FreeEnergy protocols, where 1 indicates the second TI region.
soft_core (bool) – Whether to get the record for the soft-core part of the system for the chosen region.

Returns:

records – The dictionary of time-series records.

Return type:

MultiDict

getCurrentRestraintEnergy(time_series=False, region=0, soft_core=False)[source]¶

Get the current restraint energy.

Parameters:

time_series (bool) – Whether to return a list of time series records.
region (int) – The region to which the record corresponds. There will only be more than one region for FreeEnergy protocols, where 1 indicates the second TI region.
soft_core (bool) – Whether to get the record for the soft-core part of the system for the chosen region.
block (bool) – Whether to block until the process has finished running.

Returns:

energy – The restraint energy.

Return type:

Energy

getCurrentStep(time_series=False, region=0, soft_core=False)[source]¶

Get the current number of integration steps.

Parameters:

time_series (bool) – Whether to return a list of time series records.
region (int) – The region to which the record corresponds. There will only be more than one region for FreeEnergy protocols, where 1 indicates the second TI region.
soft_core (bool) – Whether to get the record for the soft-core part of the system for the chosen region.

Returns:

step – The current number of integration steps.

Return type:

int

getCurrentSystem()[source]¶

Get the latest molecular system.

Returns:: system – The latest molecular system.
Return type:: System

getCurrentTemperature(time_series=False, region=0, soft_core=False)[source]¶

Get the current temperature.

Parameters:

time_series (bool) – Whether to return a list of time series records.
region (int) – The region to which the record corresponds. There will only be more than one region for FreeEnergy protocols, where 1 indicates the second TI region.
soft_core (bool) – Whether to get the record for the soft-core part of the system for the chosen region.

Returns:

temperature – The temperature.

Return type:

Temperature

getCurrentTime(time_series=False, region=0, soft_core=False)[source]¶

Get the current simulation time.

Parameters:

time_series (bool) – Whether to return a list of time series records.
region (int) – The region to which the record corresponds. There will only be more than one region for FreeEnergy protocols, where 1 indicates the second TI region.
soft_core (bool) – Whether to get the record for the soft-core part of the system for the chosen region.

Returns:

time – The current simulation time in nanoseconds.

Return type:

Time

getCurrentTotalEnergy(time_series=False, region=0, soft_core=False)[source]¶

Get the current total energy.

Parameters:

time_series (bool) – Whether to return a list of time series records.
region (int) – The region to which the record corresponds. There will only be more than one region for FreeEnergy protocols, where 1 indicates the second TI region.
soft_core (bool) – Whether to get the record for the soft-core part of the system for the chosen region.

Returns:

energy – The total energy.

Return type:

Energy

getCurrentVanDerWaalsEnergy(time_series=False, region=0, soft_core=False)[source]¶

Get the current Van der Vaals energy.

Parameters:

time_series (bool) – Whether to return a list of time series records.
region (int) – The region to which the record corresponds. There will only be more than one region for FreeEnergy protocols, where 1 indicates the second TI region.
soft_core (bool) – Whether to get the record for the soft-core part of the system for the chosen region.

Returns:

energy – The Van der Vaals energy.

Return type:

Energy

getCurrentVanDerWaalsEnergy14(time_series=False, region=0, soft_core=False)[source]¶

Get the current Van der Vaals energy between atoms 1 and 4.

Parameters:

time_series (bool) – Whether to return a list of time series records.
region (int) – The region to which the record corresponds. There will only be more than one region for FreeEnergy protocols, where 1 indicates the second TI region.
soft_core (bool) – Whether to get the record for the soft-core part of the system for the chosen region.

Returns:

energy – The Van der Vaals energy between atoms 1 and 4.

Return type:

Energy

getCurrentVirial(time_series=False, region=0, soft_core=False)[source]¶

Get the current virial.

Parameters:

time_series (bool) – Whether to return a list of time series records.
region (int) – The region to which the record corresponds. There will only be more than one region for FreeEnergy protocols, where 1 indicates the second TI region.
soft_core (bool) – Whether to get the record for the soft-core part of the system for the chosen region.

Returns:

virial – The virial.

Return type:

float

getCurrentVolume(time_series=False, region=0, soft_core=False)[source]¶

Get the current volume.

Parameters:

time_series (bool) – Whether to return a list of time series records.
region (int) – The region to which the record corresponds. There will only be more than one region for FreeEnergy protocols, where 1 indicates the second TI region.
soft_core (bool) – Whether to get the record for the soft-core part of the system for the chosen region.

Returns:

volume – The volume.

Return type:

Volume

getDVDL(time_series=False, region=0, soft_core=False, block='AUTO')[source]¶

Get the gradient of the total energy with respect to lambda.

Parameters:

time_series (bool) – Whether to return a list of time series records.
region (int) – The region to which the record corresponds. There will only be more than one region for FreeEnergy protocols, where 1 indicates the second TI region.
soft_core (bool) – Whether to get the record for the soft-core part of the system for the chosen region.
block (bool) – Whether to block until the process has finished running.

Returns:

dv_dl – The gradient of the total energy with respect to lambda.

Return type:

float

getDensity(time_series=False, region=0, soft_core=False, block='AUTO')[source]¶

Get the density.

Parameters:

time_series (bool) – Whether to return a list of time series records.
region (int) – The region to which the record corresponds. There will only be more than one region for FreeEnergy protocols, where 1 indicates the second TI region.
soft_core (bool) – Whether to get the record for the soft-core part of the system for the chosen region.
block (bool) – Whether to block until the process has finished running.

Returns:

density – The density.

Return type:

float

getDihedralEnergy(time_series=False, region=0, soft_core=False, block='AUTO')[source]¶

Get the total dihedral energy (proper + improper).

Parameters:

time_series (bool) – Whether to return a list of time series records.
region (int) – The region to which the record corresponds. There will only be more than one region for FreeEnergy protocols, where 1 indicates the second TI region.
soft_core (bool) – Whether to get the record for the soft-core part of the system for the chosen region.
block (bool) – Whether to block until the process has finished running.

Returns:

energy – The total dihedral energy.

Return type:

Energy

getElectrostaticEnergy(time_series=False, region=0, soft_core=False, block='AUTO')[source]¶

Get the electrostatic energy.

Parameters:

time_series (bool) – Whether to return a list of time series records.
region (int) – The region to which the record corresponds. There will only be more than one region for FreeEnergy protocols, where 1 indicates the second TI region.
soft_core (bool) – Whether to get the record for the soft-core part of the system for the chosen region.
block (bool) – Whether to block until the process has finished running.

Returns:

energy – The electrostatic energy.

Return type:

Energy

getElectrostaticEnergy14(time_series=False, region=0, soft_core=False, block='AUTO')[source]¶

Get the electrostatic energy between atoms 1 and 4.

Parameters:

time_series (bool) – Whether to return a list of time series records.
region (int) – The region to which the record corresponds. There will only be more than one region for FreeEnergy protocols, where 1 indicates the second TI region.
soft_core (bool) – Whether to get the record for the soft-core part of the system for the chosen region.
block (bool) – Whether to block until the process has finished running.

Returns:

energy – The electrostatic energy between atoms 1 and 4.

Return type:

Energy

getFrame(index)[source]¶

Return a specific trajectory frame.

Parameters:: index (int) – The index of the frame.
Returns:: frame – The System object of the corresponding frame.
Return type:: System

getHydrogenBondEnergy(time_series=False, region=0, soft_core=False, block='AUTO')[source]¶

Get the hydrogen bond energy.

Parameters:

time_series (bool) – Whether to return a list of time series records.
region (int) – The region to which the record corresponds. There will only be more than one region for FreeEnergy protocols, where 1 indicates the second TI region.
soft_core (bool) – Whether to get the record for the soft-core part of the system for the chosen region.
block (bool) – Whether to block until the process has finished running.

Returns:

energy – The hydrogen bond energy.

Return type:

Energy

getInput(name=None, file_link=False)¶

Return a link to a zip file containing the input files used by the process.

Parameters:

name (str) – The name of the zip file.
file_link (bool) – Whether to return a FileLink when working in Jupyter.

Returns:

output – A path, or file link, to an archive of the process input.

Return type:

str, IPython.display.FileLink

getKineticEnergy(time_series=False, region=0, soft_core=False, block='AUTO')[source]¶

Get the kinetic energy.

Parameters:

time_series (bool) – Whether to return a list of time series records.
region (int) – The region to which the record corresponds. There will only be more than one region for FreeEnergy protocols, where 1 indicates the second TI region.
soft_core (bool) – Whether to get the record for the soft-core part of the system for the chosen region.
block (bool) – Whether to block until the process has finished running.

Returns:

energy – The kinetic energy.

Return type:

Energy

getName()¶

Return the process name.

Returns:

namestr: The name of the process.

getNonBondedEnergy14(time_series=False, region=0, soft_core=False, block='AUTO')[source]¶

Get the non-bonded energy between atoms 1 and 4.

Parameters:

time_series (bool) – Whether to return a list of time series records.
region (int) – The region to which the record corresponds. There will only be more than one region for FreeEnergy protocols, where 1 indicates the second TI region.
soft_core (bool) – Whether to get the record for the soft-core part of the system for the chosen region.
block (bool) – Whether to block until the process has finished running.

Returns:

energy – The non-bonded energy between atoms 1 and 4.

Return type:

Energy

getOutput(name=None, block='AUTO', file_link=False)¶

Return a link to a zip file of the working directory.

Parameters:

name (str) – The name of the zip file.
block (bool) – Whether to block until the process has finished running.
file_link (bool) – Whether to return a FileLink when working in Jupyter.

Returns:

output – A path, or file link, to an archive of the process output.

Return type:

str, IPython.display.FileLink

getPackageName()¶

Return the package name.

Returns:: name – The name of the package.
Return type:: str

getPotentialEnergy(time_series=False, region=0, soft_core=False, block='AUTO')[source]¶

Get the potential energy.

Parameters:

time_series (bool) – Whether to return a list of time series records.
region (int) – The region to which the record corresponds. There will only be more than one region for FreeEnergy protocols, where 1 indicates the second TI region.
soft_core (bool) – Whether to get the record for the soft-core part of the system for the chosen region.
block (bool) – Whether to block until the process has finished running.

Returns:

energy – The potential energy.

Return type:

Energy

getPressure(time_series=False, region=0, soft_core=False, block='AUTO')[source]¶

Get the pressure.

Parameters:

time_series (bool) – Whether to return a list of time series records.
region (int) – The region to which the record corresponds. There will only be more than one region for FreeEnergy protocols, where 1 indicates the second TI region.
soft_core (bool) – Whether to get the record for the soft-core part of the system for the chosen region.
block (bool) – Whether to block until the process has finished running.

Returns:

pressure – The pressure.

Return type:

Pressure

getRecord(key, time_series=False, unit=None, region=0, soft_core=False, block='AUTO')[source]¶

Get a record from the stdout dictionary.

Parameters:

key (str) – A universal record key based on the key used in the AMBER standard output. Use ‘getRecordKey(record)` to generate the key. The records are those used in the AMBER standard output, e.g. ‘TEMP(K)’. Please consult the current AMBER manual for details: https://ambermd.org/Manuals.php
time_series (bool) – Whether to return a list of time series records.
unit (Unit) – The unit to convert the record to.
region (int) – The region to which the record corresponds. There will only be more than one region for FreeEnergy protocols, where 1 indicates the second TI region.
soft_core (bool) – Whether to get the record for the soft-core part of the system for the chosen region.
block (bool) – Whether to block until the process has finished running.

Returns:

record – The matching record.

Return type:

Type

getRecordKey(record, region=0, soft_core=False)[source]¶

Parameters:

record (str) – The record used in the AMBER standard output, e.g. ‘TEMP(K)’. Please consult the current AMBER manual for details: https://ambermd.org/Manuals.php
region (int) – The region to which the record corresponds. There will only be more than one region for FreeEnergy protocols, where 1 indicates the second TI region.
soft_core (bool) – Whether to get the record for the soft-core part of the system for the chosen region.

Returns:

key – The universal record key that can be used with getRecord.

Return type:

str

getRecords(region=0, soft_core=False, block='AUTO')[source]¶

Return the dictionary of stdout time-series records.

Parameters:

region (int) – The region to which the record corresponds. There will only be more than one region for FreeEnergy protocols, where 1 indicates the second TI region.
soft_core (bool) – Whether to get the record for the soft-core part of the system for the chosen region.
block (bool) – Whether to block until the process has finished running.

Returns:

records – The dictionary of time-series records.

Return type:

MultiDict

getRestraintEnergy(time_series=False, region=0, soft_core=False, block='AUTO')[source]¶

Get the restraint energy.

Parameters:

time_series (bool) – Whether to return a list of time series records.
region (int) – The region to which the record corresponds. There will only be more than one region for FreeEnergy protocols, where 1 indicates the second TI region.
soft_core (bool) – Whether to get the record for the soft-core part of the system for the chosen region.
block (bool) – Whether to block until the process has finished running.

Returns:

energy – The restraint energy.

Return type:

Energy

getSeed()¶

Return the random number seed.

Returns:: seed – The random number seed.
Return type:: int

getStderr(block='AUTO')¶

Return the entire stderr for the process as a list of strings.

Parameters:: block (bool) – Whether to block until the process has finished running.
Returns:: error – The list of stderror strings.
Return type:: [str]

getStdout(block='AUTO')¶

Return the entire stdout for the process as a list of strings.

Parameters:: block (bool) – Whether to block until the process has finished running.
Returns:: output – The list of stdout strings.
Return type:: [str]

getStep(time_series=False, region=0, soft_core=False, block='AUTO')[source]¶

Get the number of integration steps.

Parameters:

time_series (bool) – Whether to return a list of time series records.
region (int) – The region to which the record corresponds. There will only be more than one region for FreeEnergy protocols, where 1 indicates the second TI region.
soft_core (bool) – Whether to get the record for the soft-core part of the system for the chosen region.
block (bool) – Whether to block until the process has finished running.

Returns:

step – The current number of integration steps.

Return type:

int

getSystem(block='AUTO')[source]¶

Get the latest molecular system.

Parameters:: block (bool) – Whether to block until the process has finished running.
Returns:: system – The latest molecular system.
Return type:: System

getTemperature(time_series=False, region=0, soft_core=False, block='AUTO')[source]¶

Get the temperature.

Parameters:

time_series (bool) – Whether to return a list of time series records.
region (int) – The region to which the record corresponds. There will only be more than one region for FreeEnergy protocols, where 1 indicates the second TI region.
soft_core (bool) – Whether to get the record for the soft-core part of the system for the chosen region.
block (bool) – Whether to block until the process has finished running.

Returns:

temperature – The temperature.

Return type:

Temperature

getTime(time_series=False, region=0, soft_core=False, block='AUTO')[source]¶

Get the simulation time.

Parameters:

time_series (bool) – Whether to return a list of time series records.
region (int) – The region to which the record corresponds. There will only be more than one region for FreeEnergy protocols, where 1 indicates the second TI region.
soft_core (bool) – Whether to get the record for the soft-core part of the system for the chosen region.
block (bool) – Whether to block until the process has finished running.

Returns:

time – The current simulation time in nanoseconds.

Return type:

Time

getTotalEnergy(time_series=False, region=0, soft_core=False, block='AUTO')[source]¶

Get the total energy.

Parameters:

time_series (bool) – Whether to return a list of time series records.
region (int) – The region to which the record corresponds. There will only be more than one region for FreeEnergy protocols, where 1 indicates the second TI region.
soft_core (bool) – Whether to get the record for the soft-core part of the system for the chosen region.
block (bool) – Whether to block until the process has finished running.

Returns:

energy – The total energy.

Return type:

Energy

getTrajectory(backend='AUTO', block='AUTO')[source]¶

Return a trajectory object.

Parameters:

backend (str) – The backend to use for trajectory parsing. To see supported backends, run BioSimSpace.Trajectory.backends(). Using “AUTO” will try each in sequence.
block (bool) – Whether to block until the process has finished running.

Returns:

trajectory – The latest trajectory object.

Return type:

Trajectory

getVanDerWaalsEnergy(time_series=False, region=0, soft_core=False, block='AUTO')[source]¶

Get the Van der Vaals energy.

Parameters:

time_series (bool) – Whether to return a list of time series records.
region (int) – The region to which the record corresponds. There will only be more than one region for FreeEnergy protocols, where 1 indicates the second TI region.
soft_core (bool) – Whether to get the record for the soft-core part of the system for the chosen region.
block (bool) – Whether to block until the process has finished running.

Returns:

energy – The Van der Vaals energy.

Return type:

Energy

getVanDerWaalsEnergy14(time_series=False, region=0, soft_core=False, block='AUTO')[source]¶

Get the Van der Vaals energy between atoms 1 and 4.

Parameters:

time_series (bool) – Whether to return a list of time series records.
region (int) – The region to which the record corresponds. There will only be more than one region for FreeEnergy protocols, where 1 indicates the second TI region.
soft_core (bool) – Whether to get the record for the soft-core part of the system for the chosen region.
block (bool) – Whether to block until the process has finished running.

Returns:

energy – The Van der Vaals energy between atoms 1 and 4.

Return type:

Energy

getVirial(time_series=False, region=0, soft_core=False, block='AUTO')[source]¶

Get the virial.

Parameters:

time_series (bool) – Whether to return a list of time series records.
region (int) – The region to which the record corresponds. There will only be more than one region for FreeEnergy protocols, where 1 indicates the second TI region.
soft_core (bool) – Whether to get the record for the soft-core part of the system for the chosen region.
block (bool) – Whether to block until the process has finished running.

Returns:

virial – The virial.

Return type:

float

getVolume(time_series=False, region=0, soft_core=False, block='AUTO')[source]¶

Get the volume.

Parameters:

time_series (bool) – Whether to return a list of time series records.
region (int) – The region to which the record corresponds. There will only be more than one region for FreeEnergy protocols, where 1 indicates the second TI region.
soft_core (bool) – Whether to get the record for the soft-core part of the system for the chosen region.
block (bool) – Whether to block until the process has finished running.

Returns:

volume – The volume.

Return type:

Volume

inputFiles()¶

Return the list of input files.

Returns:: input_files – The list of autogenerated input files.
Return type:: [str]

insertArg(arg, value, index)¶

Insert a command-line argument at a specific index.

Parameters:

arg (str) – The argument to set.
value – The value of the argument.
index (int) – The index in the dictionary.

isError()¶

Return whether the process exited with an error.

Returns:: is_error – Whether the process exited with an error.
Return type:: bool

isQueued()¶

Return whether the process is queued.

Returns:: is_queued – Whether the process is queued.
Return type:: bool

isRunning()¶

Return whether the process is running.

Returns:: is_running – Whether the process is running.
Return type:: bool

kill()[source]¶: Kill the running process.

resetArgs()¶: Reset the command-line arguments.

resetConfig()¶: Reset the configuration parameters.

run(system=None, protocol=None, auto_start=True, restart=False)¶

Create and run a new process.

Parameters:

system (System) – The molecular system.
protocol (Protocol) – The simulation protocol.
auto_start (bool) – Whether to start the process automatically.
restart (bool) – Whether to restart the simulation, i.e. use the original system.

Returns:

process – The new process object.

Return type:

Procees

runTime()¶

Return the running time for the process (in minutes).

Returns:: runtime – The runtime in minutes.
Return type:: Time

setArg(arg, value)¶

Set a specific command-line argument.

For command-line flags, i.e. boolean arguments, the key should specify whether the flag is enabled (True) or not (False).

Parameters:

arg (str) – The argument to set.
value (bool, str) – The value of the argument.

setArgs(args)¶

Set the dictionary of command-line arguments.

Parameters:: args (dict, collections.OrderedDict) – A dictionary of command-line arguments.

setConfig(config)¶

Set the list of configuration file strings.

Parameters:: config (str, [str]) – The list of configuration strings, or a path to a configuration file.

setName(name)¶

Set the process name.

Parameters:: name (str) – The process name.

setSeed(seed)¶

Set the random number seed.

Parameters:: seed (int) – The random number seed.

start()[source]¶

Start the AMBER process.

Returns:: process – The process object.
Return type:: Process.Amber

stderr(n=10)¶

Print the last n lines of the stderr buffer.

Parameters:: n (int) – The number of lines to print.

stdout(n=10)[source]¶

Print the last n lines of the stdout buffer.

Parameters:: n (int) – The number of lines to print.

wait(max_time=None)¶

Wait for the process to finish.

Parameters:: max_time (Time, int, float) – The maximum time to wait (in minutes).

workDir()¶

Return the working directory.

Returns:: work_dir – The path of the working directory.
Return type:: str

writeConfig(file)¶

Write the configuration to file.

Parameters:: file (str) – The path to a file.